Multiple testing on the GO graph {globaltest} | R Documentation |
Three function to test (part of) the GO graph for association of the gene expression profile of GO terms with a response variable. Used together, these functions return multiplicity-adjusted p-values calculated using the Focus Level procedure that preserves the structure of the GO graph.
gtGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE) makeGOstructure(data, annotation, top, only.ids, ontology = c("BP", "CC", "MF"), unreliable) getFocus(GOstructure, maxatoms = 10)
... |
Arguments describing the tests to be preformed are passed on to globaltest . |
GO |
An object of class GOstructure describing the structure of the GO
graph. This object should be created using makeGOstructure |
focus |
A vector of GO ids to describe te focus level. Typically made using getFocus . |
maxalpha |
The maximum multiplicity-adjusted p-value. The algorithm will stop when this value is exceeded. |
stopafter |
The maximum number of significant GO terms to be found. The algorithm will stop when this value is exceeded. |
verbose |
If set to TRUE , prints much more extensive progress information. |
data |
The data set for which the GOstructure object is to be made. Can be either an
exprSet or a vector of
probe indicators. |
annotation |
The name of the metaData annotation package to be used, or a vector of EntrezGene ids with the same
length as the number of genes in data . |
top |
The node to be used as top node of the GOstructure . Defaults
to one of "GO:0008150", "GO:0005575", "GO:0003674", depending on he ontology chosen. The
GOstructure object will only contain offspring of the chosen top node. |
only.ids |
A vector of GO ids. If this is supplied, GO ids not appearing in this list
will not appear in the GOstructure object. |
ontology |
The ontology to be used. One of Biological Process (BP), Cellular Component (CC) or Molecular Function (MF). |
unreliable |
Can be used to designate one or more of the GO evidence codes as unreliable. Value must be a vector containing one or more from "IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS", "NAS", "ND", "RCA", "TAS", "NR". |
GOstructure |
An object of class GOstructure . |
maxatoms |
A tuning parameter that governs the choice of the focus level. getFocus will
choose those GO terms in the focus level in such a way that all offspring gene sets of each focus level
term can be constructed as unions of no more than maxatoms atom gene sets. Default value of
maxatoms is 10. Higher values quickly lead to slower
computation. Lower values typically lead to reduced power. |
These functions should be used in the following order.
First use makeGOstructure
to make a GO graph tailored to a
specific data set. Then getFocus
can be used to choose a
focus level. Finally gtGO
performs the focus level
procedure.
The function returns a named vector of multiplicity-adjusted
p-values. Adjusted p-values of GO terms not appearing in this vector
are larger than the chosen value of maxalpha
.
gtGO
cannot be used in combination with the permutation
version of globaltest
.
Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting
For references, type: citation("globaltest")
. See
also the vignette GlobalTest.pdf included with this package.
Examples in the vignette! globaltest
,
GOstructure
, gt.multtest
.
# Breast cancer data (exprSet) from the Netherlands Cancer # Institute with small GO structure (all descendants of Cell Cycle) # See the vignette for details on making a GO structure object. data(vandeVijver) data(gostructure.vandeVijver) focus <- getFocus(gostructure.vandeVijver) adjustedP <- gtGO(vandeVijver, "Surv(TIMEsurvival, EVENTdeath)", GO = gostructure.vandeVijver, focus = focus) # The significant GO graph can be visualized using # the GOstats and Rgraphviz packages. # See the vignette for details. Type: vignette("GlobalTest")